Genetic Alterations Associated with Type I Diabetes and Methods of Use Thereof for Diagnosis and Treatment

ABSTRACT

Compositions and methods for the detection and treatment of T1D are provided.

This application claims priority to U.S. Provisional Application61/103,709 filed Oct. 8, 2008, the entire contents being incorporatedherein by reference as though set forth in full.

FIELD OF THE INVENTION

This invention relates to the fields of glucose metabolism, genetics andpathology associated with diabetes, particularly type I diabetes. Morespecifically, the invention provides a panel of genes containing copynumber variations which had heretofore not been associated with thisdisease. Methods and kits for using the sequences so identified fordiagnostic and therapeutic treatment purposes are also provided, as aretherapeutic compositions for management of diabetes.

BACKGROUND OF THE INVENTION

Several publications and patent documents are cited throughout thespecification in order to describe the state of the art to which thisinvention pertains. Each of these citations is incorporated herein byreference as though set forth in full.

Type I diabetes (T1D) results from the autoimmune destruction ofpancreatic beta cells, a process believed to be strongly influenced bymultiple genes and environmental factors. The incidence of T1D has beenincreasing in Western countries and has more than doubled in the UnitedStates over the past 30 years. The disease shows a strong familialcomponent, with first-degree relatives of cases being at 15 timesgreater risk of T1D than a randomly selected member of the generalpopulation and monozygotic twins being concordant for T1D at a frequencyof approximately 50%. However, while the genetic evidence is strong, thelatter data suggests that an interplay with environmental factors alsoplays a key role in influencing T1D outcome.

The familial clustering of T1D is influenced by multiple genes.Variation in four loci has already been established to account for asignificant proportion of the familial aggregation of T1D. These includethe major histocompatibility complex (MHC) region on 6p21 (including theHLA-DRB1, -DQA 1 and -DRQ1 genes¹); the insulin/insulin-like growthfactor 2 gene complex (INS-IGF2) on 11p15²⁻⁴, the protein tyrosinephosphatase-22 (PTPN22) gene on 1p13^(5,6) and the gene encodingcytotoxic T-lymphocyte-associated protein 4 (CTLA4) on 2q31^(7,8). Theinterleukin-2 receptor alpha (CD25) locus on 10p15⁹ has also beenimplicated in the pathogenesis of T1D but remains to be replicated byindependent studies. In addition, spontaneous mouse model studies of T1Dhave implicated numerous other regions that have been confirmed inreplication studies¹⁰. Several other loci have also been implicated inhuman association studies with T1D but the effects of these implicatedgenes remain controversial and are subject to confirmation inindependent studies utilizing sufficient sample sizes. Together, thesestudies suggest that many more T1D susceptibility genes remain to bediscovered. It is also clear that there are differences in geneticsusceptibility to T1D between populations. An explanation for thisvariation may be related to differing frequencies of T1D causative andprotective variants between different populations and ethnic groups, ahypothesis that needs to be addressed in multi-center, multi-nationalstudies that are truly trans-continental.

SUMMARY OF THE INVENTION

In accordance with the present invention, T1D-associated copy numbervariations (CNVs) have been identified which are indicative of anincreased risk of developing T1D. Thus, in one aspect, nucleic acidscomprising at least one genetic alteration identified in Table 1 isprovided. Such nucleic acids and the proteins encoded thereby haveutility in the diagnosis and management of type 1 diabetes (T1D).

In another aspect of the invention, methods for assessing susceptibilityfor developing T1D are provided. An exemplary method entails providing atarget nucleic acid from a patient sample, said target nucleic acidhaving a predetermined sequence in the normal population, and assessingsaid target nucleic acid for the presence of a genetic alterationincluding one or more copy number variations which is/are indicative ofan increased risk of developing T1D. Such genetic alterations include,without limitation, inversion, deletion, duplication, and insertion ofat least one nucleotide in said sequence.

Preferably, the genetic alteration is a copy number variation listed inTable 1, the presence of which being associated with an increased riskof developing T1D.

The methods of the invention also include the detection of any of theT1D associated genetic alterations comprising the CNVs set forth inTable 1 for the diagnosis of T1D. Kits and microarrays for practicingthe foregoing methods are also provided.

In yet another embodiment, a method of managing T1D is provided whichentails administering a therapeutic agent to a patient in need thereof.The therapeutic agent can be a small molecule, an antibody, a protein,an oligonucleotide, or a siRNA molecule.

In another aspect of the invention, a method for identifying agents thatbind and/or modulate the functional activity of the protein productsencoded by the genes listed in Table 1 is provided, as well aspharmaceutical compositions comprising said agent in a biologicallyacceptable carrier.

DETAILED DESCRIPTION OF THE INVENTION

In previous studies, a number of genetic determinants of T1D have beenestablished through candidate gene studies, primarily with the majorhistocompatibility complex (MHC) but also with other loci. As describedherein, several new genetic alterations have been discovered whichpredispose the patient to an increased risk for TID. These resultsprovide evidence for a diverse set of genetic factors that contributesubstantially to the pathogenesis of T1D, and thus provide promising newT1D therapeutic and diagnostic targets.

The following definitions are provided to facilitate an understanding ofthe present invention:

For purposes of the present invention, “a” or “an” entity refers to oneor more of that entity; for example, “a cDNA” refers to one or more cDNAor at least one cDNA. As such, the terms “a” or “an,” “one or more” and“at least one” can be used interchangeably herein. It is also noted thatthe terms “comprising,” “including,” and “having” can be usedinterchangeably. Furthermore, a compound “selected from the groupconsisting of” refers to one or more of the compounds in the list thatfollows, including mixtures (i.e. combinations) of two or more of thecompounds. According to the present invention, an isolated, orbiologically pure molecule is a compound that has been removed from itsnatural milieu. As such, “isolated” and “biologically pure” do notnecessarily reflect the extent to which the compound has been purified.An isolated compound of the present invention can be obtained from itsnatural source, can be produced using laboratory synthetic techniques orcan be produced by any such chemical synthetic route.

A “copy number variation (CNV)” refers to the number of copies of aparticular gene in the genotype of an individual. CNVs represent a majorgenetic component of human phenotypic diversity. Susceptibility togenetic disorders is known to be associated not only with singlenucleotide polymorphisms (SNP), but also with structural and othergenetic variations, including CNVs. A CNV represents a copy numberchange involving a DNA fragment that is ˜1 kilobases (kb) or larger(Feuk et al. 2006 Hum. Mol. Genet., 15: R57-R66). CNVs described hereindo not include those variants that arise from the insertion/deletion oftransposable elements (e.g., ˜6-kb KpnI repeats) to minimize thecomplexity of future CNV analyses. The term CNV therefore encompassespreviously introduced terms such as large-scale copy number variants(LCVs; Iafrate et al. 2004 Nature Genetics 36: 949-51), copy numberpolymorphisms (CNPs; Sebat et al. 2004 Science 305: 525-528.), andintermediate-sized variants (ISVs; Tuzun et al. 2005 Nat Genet.37:727-32), but not retroposon insertions.

A “single nucleotide polymorphism (SNP)” refers to a change in which asingle base in the DNA differs from the usual base at that position.These single base changes are called SNPs or “snips.” Millions of SNP'shave been cataloged in the human genome. Some SNPs, such as that whichcauses sickle cell, are responsible for disease. Other SNPs are normalvariations in the genome. Finally, some SNPs, are indicative of apredisposition to certain diseases (e.g., T1D).

The term “genetic alteration” as used herein refers to a change from thewild-type or reference sequence of one or more nucleic acid molecules.Genetic alterations include without limitation, base pair substitutions,additions and deletions of at least one nucleotide from a nucleic acidmolecule of known sequence.

The phrase “Type 1 diabetes (T1D)” refers to a chronic (lifelong)disease that occurs when the pancreas produces too little insulin toregulate blood sugar levels appropriately. T1D, often called juvenile orinsulin-dependent diabetes results from altered metabolism ofcarbohydrates (including sugars such as glucose), proteins, and fats. Intype 1 diabetes, the beta cells of the pancreas produce little or noinsulin, the hormone that allows glucose to enter body cells. Onceglucose enters a cell, it is used as fuel. Without adequate insulin,glucose builds up in the bloodstream instead of going into the cells.The body is unable to use this glucose for energy despite high levels inthe bloodstream, leading to increased hunger. In addition, the highlevels of glucose in the blood cause the patient to urinate more, whichin turn causes excessive thirst. Within 5 to 10 years after diagnosis,the insulin-producing beta cells of the pancreas are completelydestroyed, and no more insulin is produced.

“T1D-associated CNV or specific marker” is a CNV or marker which isassociated with an increased risk of developing TID not found normalpatients who do not have this disease. Such markers may include but arenot limited to nucleic acids, proteins encoded thereby, or other smallmolecules. Type 1 diabetes can occur at any age, but it usually startsin people younger than 30. Symptoms are usually severe and occurrapidly. The exact cause of type 1 diabetes is not known. Type 1diabetes accounts for 3% of all new cases of diabetes each year. Thereis 1 new case per every 7,000 children per year. New cases are lesscommon among adults older than 20.

The term “solid matrix” as used herein refers to any format, such asbeads, microparticles, a microarray, the surface of a microtitrationwell or a test tube, a dipstick or a filter. The material of the matrixmay be polystyrene, cellulose, latex, nitrocellulose, nylon,polyacrylamide, dextran or agarose. “Sample” or “patient sample” or“biological sample” generally refers to a sample which may be tested fora particular molecule, preferably an T1D specific marker molecule, suchas a marker shown in the table provided below. Samples may include butare not limited to cells, body fluids, including blood, serum, plasma,urine, saliva, tears, pleural fluid and the like.

The phrase “consisting essentially of” when referring to a particularnucleotide or amino acid means a sequence having the properties of agiven SEQ ID NO. For example, when used in reference to an amino acidsequence, the phrase includes the sequence per se and molecularmodifications that would not affect the functional and novelcharacteristics of the sequence.

“Target nucleic acid” as used herein refers to a previously definedregion of a nucleic acid present in a complex nucleic acid mixturewherein the defined wild-type region contains at least one knownnucleotide variation which appears to be associated with T1D. Thenucleic acid molecule may be isolated from a natural source by cDNAcloning or subtractive hybridization or synthesized manually. Thenucleic acid molecule may be synthesized manually by the triestersynthetic method or by using an automated DNA synthesizer.

With regard to nucleic acids used in the invention, the term “isolatednucleic acid” is sometimes employed. This term, when applied to DNA,refers to a DNA molecule that is separated from sequences with which itis immediately contiguous (in the 5′ and 3′ directions) in the naturallyoccurring genome of the organism from which it was derived. For example,the “isolated nucleic acid” may comprise a DNA molecule inserted into avector, such as a plasmid or virus vector, or integrated into thegenomic DNA of a prokaryote or eukaryote. An “isolated nucleic acidmolecule” may also comprise a cDNA molecule. An isolated nucleic acidmolecule inserted into a vector is also sometimes referred to herein asa recombinant nucleic acid molecule.

With respect to RNA molecules, the term “isolated nucleic acid”primarily refers to an RNA molecule encoded by an isolated DNA moleculeas defined above. Alternatively, the term may refer to an RNA moleculethat has been sufficiently separated from RNA molecules with which itwould be associated in its natural state (i.e., in cells or tissues),such that it exists in a “substantially pure” form.

By the use of the term “enriched” in reference to nucleic acid it ismeant that the specific DNA or RNA sequence constitutes a significantlyhigher fraction (2-5 fold) of the total DNA or RNA present in the cellsor solution of interest than in normal cells or in the cells from whichthe sequence was taken. This could be caused by a person by preferentialreduction in the amount of other DNA or RNA present, or by apreferential increase in the amount of the specific DNA or RNA sequence,or by a combination of the two. However, it should be noted that“enriched” does not imply that there are no other DNA or RNA sequencespresent, just that the relative amount of the sequence of interest hasbeen significantly increased.

It is also advantageous for some purposes that a nucleotide sequence bein purified form. The term “purified” in reference to nucleic acid doesnot require absolute purity (such as a homogeneous preparation);instead, it represents an indication that the sequence is relativelypurer than in the natural environment (compared to the natural level,this level should be at least 2-5 fold greater, e.g., in terms ofmg/ml). Individual clones isolated from a cDNA library may be purifiedto electrophoretic homogeneity. The claimed DNA molecules obtained fromthese clones can be obtained directly from total DNA or from total RNA.The cDNA clones are not naturally occurring, but rather are preferablyobtained via manipulation of a partially purified naturally occurringsubstance (messenger RNA). The construction of a cDNA library from mRNAinvolves the creation of a synthetic substance (cDNA) and pureindividual cDNA clones can be isolated from the synthetic library byclonal selection of the cells carrying the cDNA library. Thus, theprocess which includes the construction of a cDNA library from mRNA andisolation of distinct cDNA clones yields an approximately 10⁻⁶-foldpurification of the native message. Thus, purification of at least oneorder of magnitude, preferably two or three orders, and more preferablyfour or five orders of magnitude is expressly contemplated. Thus, theterm “substantially pure” refers to a preparation comprising at least50-60% by weight the compound of interest (e.g., nucleic acid,oligonucleotide, etc.). More preferably, the preparation comprises atleast 75% by weight, and most preferably 90-99% by weight, the compoundof interest. Purity is measured by methods appropriate for the compoundof interest.

The term “complementary” describes two nucleotides that can formmultiple favorable interactions with one another. For example, adenineis complementary to thymine as they can form two hydrogen bonds.Similarly, guanine and cytosine are complementary since they can formthree hydrogen bonds. Thus if a nucleic acid sequence contains thefollowing sequence of bases, thymine, adenine, guanine and cytosine, a“complement” of this nucleic acid molecule would be a moleculecontaining adenine in the place of thymine, thymine in the place ofadenine, cytosine in the place of guanine, and guanine in the place ofcytosine. Because the complement can contain a nucleic acid sequencethat forms optimal interactions with the parent nucleic acid molecule,such a complement can bind with high affinity to its parent molecule.

With respect to single stranded nucleic acids, particularlyoligonucleotides, the term “specifically hybridizing” refers to theassociation between two single-stranded nucleotide molecules ofsufficiently complementary sequence to permit such hybridization underpre-determined conditions generally used in the art (sometimes termed“substantially complementary”). In particular, the term refers tohybridization of an oligonucleotide with a substantially complementarysequence contained within a single-stranded DNA or RNA molecule of theinvention, to the substantial exclusion of hybridization of theoligonucleotide with single-stranded nucleic acids of non-complementarysequence. For example, specific hybridization can refer to a sequencewhich hybridizes to any T1D specific marker gene or nucleic acid, butdoes not hybridize to other human nucleotides. Also polynucleotide which“specifically hybridizes” may hybridize only to a T1D specific marker,such a T1D-specific marker shown in Table 1. Appropriate conditionsenabling specific hybridization of single stranded nucleic acidmolecules of varying complementarity are well known in the art.

For instance, one common formula for calculating the stringencyconditions required to achieve hybridization between nucleic acidmolecules of a specified sequence homology is set forth below (Sambrooket al., Molecular Cloning, Cold Spring Harbor Laboratory (1989):

T _(m)=81.5° C.+16.6 Log [Na+]+0.41(%G+C)−0.63(%formamide)−600/#bp induplex

As an illustration of the above formula, using [Na+]=[0.368] and 50%formamide, with GC content of 42% and an average probe size of 200bases, the T_(m) is 57° C. The T_(m) of a DNA duplex decreases by 1-1.5°C. with every 1% decrease in homology. Thus, targets with greater thanabout 75% sequence identity would be observed using a hybridizationtemperature of 42° C.

The stringency of the hybridization and wash depend primarily on thesalt concentration and temperature of the solutions. In general, tomaximize the rate of annealing of the probe with its target, thehybridization is usually carried out at salt and temperature conditionsthat are 20-25° C. below the calculated T_(m) of the hybrid. Washconditions should be as stringent as possible for the degree of identityof the probe for the target. In general, wash conditions are selected tobe approximately 12-20° C. below the T_(m) of the hybrid. In regards tothe nucleic acids of the current invention, a moderate stringencyhybridization is defined as hybridization in 6×SSC, 5×Denhardt'ssolution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA at 42° C.,and washed in 2×SSC and 0.5% SDS at 55° C. for 15 minutes. A highstringency hybridization is defined as hybridization in 6×SSC,5×Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNAat 42° C., and washed in 1×SSC and 0.5% SDS at 65° C. for 15 minutes. Avery high stringency hybridization is defined as hybridization in 6×SSC,5×Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNAat 42° C., and washed in 0.1×SSC and 0.5% SDS at 65° C. for 15 minutes.

The term “oligonucleotide” or “oligo” as used herein means a shortsequence of DNA or DNA derivatives typically 8 to 35 nucleotides inlength, primers, or probes. An oligonucleotide can be derivedsynthetically, by cloning or by amplification. An oligo is defined as anucleic acid molecule comprised of two or more ribo- ordeoxyribonucleotides, preferably more than three. The exact size of theoligonucleotide will depend on various factors and on the particularapplication and use of the oligonucleotide. The term “derivative” isintended to include any of the above described variants when comprisingan additional chemical moiety not normally a part of these molecules.These chemical moieties can have varying purposes including, improvingsolubility, absorption, biological half life, decreasing toxicity andeliminating or decreasing undesirable side effects.

The term “probe” as used herein refers to an oligonucleotide,polynucleotide or nucleic acid, either RNA or DNA, whether occurringnaturally as in a purified restriction enzyme digest or producedsynthetically, which is capable of annealing with or specificallyhybridizing to a nucleic acid with sequences complementary to the probe.A probe may be either single-stranded or double-stranded. The exactlength of the probe will depend upon many factors, includingtemperature, source of probe and use of the method. For example, fordiagnostic applications, depending on the complexity of the targetsequence, the oligonucleotide probe typically contains 15-25 or morenucleotides, although it may contain fewer nucleotides. The probesherein are selected to be complementary to different strands of aparticular target nucleic acid sequence. This means that the probes mustbe sufficiently complementary so as to be able to “specificallyhybridize” or anneal with their respective target strands under a set ofpre-determined conditions. Therefore, the probe sequence need notreflect the exact complementary sequence of the target. For example, anon-complementary nucleotide fragment may be attached to the 5′ or 3′end of the probe, with the remainder of the probe sequence beingcomplementary to the target strand. Alternatively, non-complementarybases or longer sequences can be interspersed into the probe, providedthat the probe sequence has sufficient complementarity with the sequenceof the target nucleic acid to anneal therewith specifically.

The term “primer” as used herein refers to an oligonucleotide, eitherRNA or DNA, either single-stranded or double-stranded, either derivedfrom a biological system, generated by restriction enzyme digestion, orproduced synthetically which, when placed in the proper environment, isable to functionally act as an initiator of template-dependent nucleicacid synthesis. When presented with an appropriate nucleic acidtemplate, suitable nucleoside triphosphate precursors of nucleic acids,a polymerase enzyme, suitable cofactors and conditions such as asuitable temperature and pH, the primer may be extended at its 3′terminus by the addition of nucleotides by the action of a polymerase orsimilar activity to yield a primer extension product. The primer mayvary in length depending on the particular conditions and requirement ofthe application. For example, in diagnostic applications, theoligonucleotide primer is typically 15-25 or more nucleotides in length.The primer must be of sufficient complementarity to the desired templateto prime the synthesis of the desired extension product, that is, to beable anneal with the desired template strand in a manner sufficient toprovide the 3′ hydroxyl moiety of the primer in appropriatejuxtaposition for use in the initiation of synthesis by a polymerase orsimilar enzyme. It is not required that the primer sequence represent anexact complement of the desired template. For example, anon-complementary nucleotide sequence may be attached to the 5′ end ofan otherwise complementary primer. Alternatively, non-complementarybases may be interspersed within the oligonucleotide primer sequence,provided that the primer sequence has sufficient complementarity withthe sequence of the desired template strand to functionally provide atemplate-primer complex for the synthesis of the extension product.

Polymerase chain reaction (PCR) has been described in U.S. Pat. Nos.4,683,195, 4,800,195, and 4,965,188, the entire disclosures of which areincorporated by reference herein.

An “siRNA” refers to a molecule involved in the RNA interference processfor a sequence-specific post-transcriptional gene silencing or geneknockdown by providing small interfering RNAs (siRNAs) that has homologywith the sequence of the targeted gene. Small interfering RNAs (siRNAs)can be synthesized in vitro or generated by ribonuclease III cleavagefrom longer dsRNA and are the mediators of sequence-specific mRNAdegradation. Preferably, the siRNA of the invention are chemicallysynthesized using appropriately protected ribonucleosidephosphoramidites and a conventional DNA/RNA synthesizer. The siRNA canbe synthesized as two separate, complementary RNA molecules, or as asingle RNA molecule with two complementary regions. Commercial suppliersof synthetic RNA molecules or synthesis reagents include AppliedBiosystems (Foster City, Calif., USA), Proligo (Hamburg, Germany),Dharmacon Research (Lafayette, Colo., USA), Pierce Chemical (part ofPerbio Science, Rockford, Ill., USA), Glen Research (Sterling, Va.,USA), ChemGenes (Ashland, Mass., USA) and Cruachem (Glasgow, UK).Specific siRNA constructs for inhibiting production of the mRNA encodingthe protein products listed in Table 1 may be between 15-35 nucleotidesin length, and more typically about 21 nucleotides in length.

The term “vector” relates to a single or double stranded circularnucleic acid molecule that can be infected, transfected or transformedinto cells and replicate independently or within the host cell genome. Acircular double stranded nucleic acid molecule can be cut and therebylinearized upon treatment with restriction enzymes. An assortment ofvectors, restriction enzymes, and the knowledge of the nucleotidesequences that are targeted by restriction enzymes are readily availableto those skilled in the art, and include any replicon, such as aplasmid, cosmid, bacmid, phage or virus, to which another geneticsequence or element (either DNA or RNA) may be attached so as to bringabout the replication of the attached sequence or element. A nucleicacid molecule of the invention can be inserted into a vector by cuttingthe vector with restriction enzymes and ligating the two piecestogether.

Many techniques are available to those skilled in the art to facilitatetransformation, transfection, or transduction of the expressionconstruct into a prokaryotic or eukaryotic organism. The terms“transformation”, “transfection”, and “transduction” refer to methods ofinserting a nucleic acid and/or expression construct into a cell or hostorganism. These methods involve a variety of techniques, such astreating the cells with high concentrations of salt, an electric field,or detergent, to render the host cell outer membrane or wall permeableto nucleic acid molecules of interest, microinjection,peptide-tethering, PEG-fusion, and the like.

The term “promoter element” describes a nucleotide sequence that isincorporated into a vector that, once inside an appropriate cell, canfacilitate transcription factor and/or polymerase binding and subsequenttranscription of portions of the vector DNA into mRNA. In oneembodiment, the promoter element of the present invention precedes the5′ end of the T1D specific marker nucleic acid molecule such that thelatter is transcribed into mRNA. Host cell machinery then translatesmRNA into a polypeptide.

Those skilled in the art will recognize that a nucleic acid vector cancontain nucleic acid elements other than the promoter element and theT1D specific marker gene nucleic acid molecule. These other nucleic acidelements include, but are not limited to, origins of replication,ribosomal binding sites, nucleic acid sequences encoding drug resistanceenzymes or amino acid metabolic enzymes, and nucleic acid sequencesencoding secretion signals, localization signals, or signals useful forpolypeptide purification.

A “replicon” is any genetic element, for example, a plasmid, cosmid,bacmid, plastid, phage or virus that is capable of replication largelyunder its own control. A replicon may be either RNA or DNA and may besingle or double stranded.

An “expression operon” refers to a nucleic acid segment that may possesstranscriptional and translational control sequences, such as promoters,enhancers, translational start signals (e.g., ATG or AUG codons),polyadenylation signals, terminators, and the like, and which facilitatethe expression of a polypeptide coding sequence in a host cell ororganism.

As used herein, the terms “reporter,” “reporter system”, “reportergene,” or “reporter gene product” shall mean an operative genetic systemin which a nucleic acid comprises a gene that encodes a product thatwhen expressed produces a reporter signal that is a readily measurable,e.g., by biological assay, immunoassay, radio immunoassay, or bycolorimetric, fluorogenic, chemiluminescent or other methods. Thenucleic acid may be either RNA or DNA, linear or circular, single ordouble stranded, antisense or sense polarity, and is operatively linkedto the necessary control elements for the expression of the reportergene product. The required control elements will vary according to thenature of the reporter system and whether the reporter gene is in theform of DNA or RNA, but may include, but not be limited to, suchelements as promoters, enhancers, translational control sequences, polyA addition signals, transcriptional termination signals and the like.

The introduced nucleic acid may or may not be integrated (covalentlylinked) into nucleic acid of the recipient cell or organism. Inbacterial, yeast, plant and mammalian cells, for example, the introducednucleic acid may be maintained as an episomal element or independentreplicon such as a plasmid. Alternatively, the introduced nucleic acidmay become integrated into the nucleic acid of the recipient cell ororganism and be stably maintained in that cell or organism and furtherpassed on or inherited to progeny cells or organisms of the recipientcell or organism. Finally, the introduced nucleic acid may exist in therecipient cell or host organism only transiently.

The term “selectable marker gene” refers to a gene that when expressedconfers a selectable phenotype, such as antibiotic resistance, on atransformed cell.

The term “operably linked” means that the regulatory sequences necessaryfor expression of the coding sequence are placed in the DNA molecule inthe appropriate positions relative to the coding sequence so as toeffect expression of the coding sequence. This same definition issometimes applied to the arrangement of transcription units and othertranscription control elements (e.g. enhancers) in an expression vector.

The terms “recombinant organism,” or “transgenic organism” refer toorganisms which have a new combination of genes or nucleic acidmolecules. A new combination of genes or nucleic acid molecules can beintroduced into an organism using a wide array of nucleic acidmanipulation techniques available to those skilled in the art. The term“organism” relates to any living being comprised of a least one cell. Anorganism can be as simple as one eukaryotic cell or as complex as amammal. Therefore, the phrase “a recombinant organism” encompasses arecombinant cell, as well as eukaryotic and prokaryotic organism.

The term “isolated protein” or “isolated and purified protein” issometimes used herein. This term refers primarily to a protein producedby expression of an isolated nucleic acid molecule of the invention.Alternatively, this term may refer to a protein that has beensufficiently separated from other proteins with which it would naturallybe associated, so as to exist in “substantially pure” form. “Isolated”is not meant to exclude artificial or synthetic mixtures with othercompounds or materials, or the presence of impurities that do notinterfere with the fundamental activity, and that may be present, forexample, due to incomplete purification, addition of stabilizers, orcompounding into, for example, immunogenic preparations orpharmaceutically acceptable preparations.

A “specific binding pair” comprises a specific binding member (sbm) anda binding partner (bp) which have a particular specificity for eachother and which in normal conditions bind to each other in preference toother molecules. Examples of specific binding pairs are antigens andantibodies, ligands and receptors and complementary nucleotidesequences. The skilled person is aware of many other examples. Further,the term “specific binding pair” is also applicable where either or bothof the specific binding member and the binding partner comprise a partof a large molecule. In embodiments in which the specific binding paircomprises nucleic acid sequences, they will be of a length to hybridizeto each other under conditions of the assay, preferably greater than 10nucleotides long, more preferably greater than 15 or 20 nucleotideslong. “Sample” or “patient sample” or “biological sample” generallyrefers to a sample which may be tested for a particular molecule,preferably a T1D specific marker molecule, such as a marker shown inTable 1. Samples may include but are not limited to cells, body fluids,including blood, serum, plasma, urine, saliva, tears, pleural fluid andthe like.

The terms “agent” and “test compound” are used interchangeably hereinand denote a chemical compound, a mixture of chemical compounds, abiological macromolecule, or an extract made from biological materialssuch as bacteria, plants, fungi, or animal (particularly mammalian)cells or tissues. Biological macromolecules include siRNA, shRNA,antisense oligonucleotides, small molecules, antibodies, peptides,peptide/DNA complexes, and any nucleic acid based molecule, for examplean oligo, which exhibits the capacity to modulate the activity of theCNV containing nucleic acids described herein or their encoded proteins.Agents are evaluated for potential biological activity by inclusion inscreening assays described herein below.

The term “modulate” as used herein refers increasing or decreasing. Forexample, the term modulate refers to the ability of a compound or testagent to interfere with signaling or activity of a gene or protein ofthe present invention. Therefore, modulating the signaling mediated by aprotein product listed in Table 1 means that an agent or compoundinhibits or enhances the activity of the proteins encoded by the gene.This includes altering the activity of natural killer cells, andpreventing autoimmune beta cell destruction.

Methods of Using T1D-Associated CNVS For T1D Detection Assays

T1D CNV containing nucleic acids, including but not limited to thoselisted in Table 1, may be used for a variety of purposes in accordancewith the present invention. T1D-associated CNV containing DNA, RNA, orfragments thereof may be used as probes to detect the presence of and/orexpression of T1D specific markers. Methods in which T1D specific markernucleic acids may be utilized as probes for such assays include, but arenot limited to: (1) in situ hybridization; (2) Southern hybridization(3) northern hybridization; and (4) assorted amplification reactionssuch as polymerase chain reactions (PCR).

Further, assays for detecting T1D-associated CNVs may be conducted onany type of biological sample, including but not limited to body fluids(including blood, urine, serum, gastric lavage), any type of cell (suchas white blood cells, mononuclear cells) or body tissue.

From the foregoing discussion, it can be seen that T1D associated CNVcontaining nucleic acids, vectors expressing the same, T1D CNVcontaining marker proteins and anti-T1D specific marker antibodies ofthe invention can be used to detect T1D associated CNVs in body tissue,cells, or fluid, and alter T1D CNV containing marker protein expressionfor purposes of assessing the genetic and protein interactions involvedin T1D.

In most embodiments for screening for T1D-associated CNVs, theT1D-associated CNV containing nucleic acid in the sample will initiallybe amplified, e.g. using PCR, to increase the amount of the template ascompared to other sequences present in the sample. This allows thetarget sequences to be detected with a high degree of sensitivity ifthey are present in the sample. This initial step may be avoided byusing highly sensitive array techniques that are becoming increasinglyimportant in the art.

Alternatively, new detection technologies can overcome this limitationand enable analysis of small samples containing as little as 1 μg oftotal RNA. Using Resonance Light Scattering (RLS) technology, as opposedto traditional fluorescence techniques, multiple reads can detect lowquantities of mRNAs using biotin labeled hybridized targets andanti-biotin antibodies. Another alternative to PCR amplificationinvolves planar wave guide technology (PWG) to increase signal-to-noiseratios and reduce background interference. Both techniques arecommercially available from Qiagen Inc. (USA).

Thus, any of the aforementioned techniques may be used to detect orquantify T1D-associated CNV marker expression and accordingly, detectpatient susceptibility for developing T1D.

Kits and Articles of Manufacture

Any of the aforementioned products can be incorporated into a kit whichmay contain an T1D-associated CNV specific marker polynucleotide or oneor more such markers immobilized on a Gene Chip, an oligonucleotide, apolypeptide, a peptide, an antibody, a label, marker, or reporter, apharmaceutically acceptable carrier, a physiologically acceptablecarrier, instructions for use, a container, a vessel for administration,an assay substrate, or any combination thereof.

Methods of Using T1D-Associated CNVS for Development of TherapeuticAgents

Since the CNVs identified herein have been associated with the etiologyof T1D, methods for identifying agents that modulate the activity of thegenes and their encoded products containing such CNVs should result inthe generation of efficacious therapeutic agents for the treatment of avariety of disorders associated with this condition.

Several of the identified genes contain regions which provide suitabletargets for the rational design of therapeutic agents which modulatetheir activity. Small peptide molecules corresponding to these regionsmay be used to advantage in the design of therapeutic agents whicheffectively modulate the activity of the encoded proteins.

Molecular modeling should facilitate the identification of specificorganic molecules with capacity to bind to the active site of theproteins encoded by the CNV containing nucleic acids based onconformation or key amino acid residues required for function. Acombinatorial chemistry approach will be used to identify molecules withgreatest activity and then iterations of these molecules will bedeveloped for further cycles of screening. Molecular modeling shouldfacilitate the identification of specific organic molecules withcapacity to bind to the active site of these proteins based onconformation or key amino acid residues required for function. Acombinatorial chemistry approach will be used to identify molecules withgreatest activity and then iterations of these molecules will bedeveloped for further cycles of screening. In certain embodiments,candidate agents can be screening from large libraries of synthetic ornatural compounds. Such compound libraries are commercially availablefrom a number of companies including but not limited to MaybridgeChemical Co., (Trevillet, Cornwall, UK), Comgenex (Princeton, N.J.),Microsour (New Milford, Conn.) Aldrich (Milwaukee, Wis.) Akos Consultingand Solutions GmbH (Basel, Switzerland), Ambinter (Paris, France),Asinex (Moscow, Russia) Aurora (Graz, Austria), BioFocus DPI(Switzerland), Bionet (Camelford, UK), Chembridge (San Diego, Calif.),Chem Div (San Diego, Calif.). The skilled person is aware of othersources and can readily purchase the same. Once therapeuticallyefficacious compounds are identified in the screening assays describedherein, they can be formulated in to pharmaceutical compositions andutilized for the treatment of cancer, alone or in combination withagents typically used to treat T1D.

The polypeptides or fragments employed in drug screening assays mayeither be free in solution, affixed to a solid support or within a cell.One method of drug screening utilizes eukaryotic or prokaryotic hostcells which are stably transformed with recombinant polynucleotidesexpressing the polypeptide or fragment, preferably in competitivebinding assays. Such cells, either in viable or fixed form, can be usedfor standard binding assays. One may determine, for example, formationof complexes between the polypeptide or fragment and the agent beingtested, or examine the degree to which the formation of a complexbetween the polypeptide or fragment and a known substrate is interferedwith by the agent being tested.

Another technique for drug screening provides high throughput screeningfor compounds having suitable binding affinity for the encodedpolypeptides and is described in detail in Geysen, PCT publishedapplication WO 84/03564, published on Sep. 13, 1984. Briefly stated,large numbers of different, small peptide test compounds, such as thosedescribed above, are synthesized on a solid substrate, such as plasticpins or some other surface. The peptide test compounds are reacted withthe target polypeptide and washed. Bound polypeptide is then detected bymethods well known in the art.

A further technique for drug screening involves the use of hosteukaryotic cell lines or cells (such as described above) which have anonfunctional or altered T1D associated gene. These host cell lines orcells are defective at the polypeptide level. The host cell lines orcells are grown in the presence of drug compound. The rate of cellularmetabolism of the host cells is measured to determine if the compound iscapable of regulating cellular metabolism in the defective cells. Hostcells contemplated for use in the present invention include but are notlimited to bacterial cells, fungal cells, insect cells, mammalian cells,and plant cells. The T1D-associated CNV encoding DNA molecules may beintroduced singly into such host cells or in combination to assess thephenotype of cells conferred by such expression. Methods for introducingDNA molecules are also well known to those of ordinary skill in the art.Such methods are set forth in Ausubel et al. eds., Current Protocols inMolecular Biology, John Wiley & Sons, NY, N.Y. 1995, the disclosure ofwhich is incorporated by reference herein.

Cells and cell lines suitable for studying the effects of the CNVencoding nucleic acids on glucose metabolism and methods of use thereoffor drug discovery are provided. Such cells and cell lines will betransfected with the CNV encoding nucleic acids described herein and theeffects on glucagon secretion, insulin secretion and/or beta cellapoptosis can be determined. Such cells and cell lines will also becontacted with the siRNA molecules provided herein to assess the effectsthereof on glucagon secretion, insulin secretion and/or beta cellapoptosis. The siRNA molecules will be tested alone and in combinationof 2, 3, 4, and 5 siRNAs to identify the most efficacious combinationfor down regulating the target gene of interest. Cells suitable forthese purposes include, without limitation, INS cells (ATCC CRL 11605),PC12 cells (ATCC CRL 1721), MIN6 cells, alpha-TC6 cells and INS-1 832/13cells (Fernandez et al., J. of Proteome Res. (2007). 7:400-411).Pancreatic islet cells can be isolated and cultured as described inJoseph, J. et al., (J. Biol. Chem. (2004) 279:51049). Diao et al. (J.Biol. Chem. (2005) 280:33487-33496), provide methodology for assessingthe effects of the CNV encoding nucleic acids and/or the siRNAs providedherein on glucagon secretion and insulin secretion. Park, J. et al. (J.of Bioch. and Mol. Biol. (2007) 40:1058-68) provide methodology forassessing the effect of these nucleic acid molecules on glucosamineinduced beta cell apoptosis in pancreatic islet cells.

A wide variety of expression vectors are available that can be modifiedto express the novel DNA or RNA sequences of this invention. Thespecific vectors exemplified herein are merely illustrative, and are notintended to limit the scope of the invention. Expression methods aredescribed by Sambrook et al. Molecular Cloning: A Laboratory Manual orCurrent Protocols in Molecular Biology 16.3-17.44 (1989). Expressionmethods in Saccharomyces are also described in Current Protocols inMolecular Biology (1989).

Suitable vectors for use in practicing the invention include prokaryoticvectors such as the pNH vectors (Stratagene Inc., 11099 N. Torrey PinesRd., La Jolla, Calif. 92037), pET vectors (Novogen Inc., 565 ScienceDr., Madison, Wis. 53711) and the pGEX vectors (Pharmacia LKBBiotechnology Inc., Piscataway, N.J. 08854). Examples of eukaryoticvectors useful in practicing the present invention include the vectorspRc/CMV, pRc/RSV, and pREP (Invitrogen, 11588 Sorrento Valley Rd., SanDiego, Calif. 92121); pcDNA3.1N5&His (Invitrogen); baculovirus vectorssuch as pVL1392, pVL1393, or pAC360 (Invitrogen); and yeast vectors suchas YRP17, YIP5, and YEP24 (New England Biolabs, Beverly, Mass.), as wellas pRS403 and pRS413 Stratagene Inc.); Picchia vectors such as pHIL-D1(Phillips Petroleum Co., Bartlesville, Okla. 74004); retroviral vectorssuch as PLNCX and pLPCX (Clontech); and adenoviral and adeno-associatedviral vectors.

Promoters for use in expression vectors of this invention includepromoters that are operable in prokaryotic or eukaryotic cells.Promoters that are operable in prokaryotic cells include lactose (lac)control elements, bacteriophage lambda (pL) control elements, arabinosecontrol elements, tryptophan (trp) control elements, bacteriophage T7control elements, and hybrids thereof. Promoters that are operable ineukaryotic cells include Epstein Barr virus promoters, adenoviruspromoters, SV40 promoters, Rous Sarcoma Virus promoters, cytomegalovirus(CMV) promoters, baculovirus promoters such as AcMNPV polyhedrinpromoter, Picchia promoters such as the alcohol oxidase promoter, andSaccharomyces promoters such as the gal4 inducible promoter and the PGKconstitutive promoter.

In addition, a vector of this invention may contain any one of a numberof various markers facilitating the selection of a transformed hostcell. Such markers include genes associated with temperaturesensitivity, drug resistance, or enzymes associated with phenotypiccharacteristics of the host organisms.

Host cells expressing the T1D-associated CNVs of the present inventionor functional fragments thereof provide a system in which to screenpotential compounds or agents for the ability to modulate thedevelopment of T1D. Thus, in one embodiment, the nucleic acid moleculesof the invention may be used to create recombinant cell lines for use inassays to identify agents which modulate the functional activity of thegenes listed in Table 1. Also provided herein are methods to screen forcompounds capable of modulating the function of proteins encoded by theCNV containing nucleic acids described below.

Another approach entails the use of phage display libraries engineeredto express fragment of the polypeptides encoded by the CNV containingnucleic acids on the phage surface. Such libraries are then contactedwith a combinatorial chemical library under conditions wherein bindingaffinity between the expressed peptide and the components of thechemical library may be detected. U.S. Pat. Nos. 6,057,098 and 5,965,456provide methods and apparatus for performing such assays.

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides of interest or of small molecules withwhich they interact (e.g., agonists, antagonists, inhibitors) in orderto fashion drugs which are, for example, more active or stable forms ofthe polypeptide, or which, e.g., enhance or interfere with the functionof a polypeptide in vivo. See, e.g., Hodgson, (1991) Bio/Technology9:19-21. In one approach, discussed above, the three-dimensionalstructure of a protein of interest or, for example, of theprotein-substrate complex, is solved by x-ray crystallography, bynuclear magnetic resonance, by computer modeling or most typically, by acombination of approaches. Less often, useful information regarding thestructure of a polypeptide may be gained by modeling based on thestructure of homologous proteins. An example of rational drug design isthe development of HIV protease inhibitors (Erickson et al., (1990)Science 249:527-533). In addition, peptides may be analyzed by analanine scan (Wells, (1991) Meth. Enzym. 202:390-411). In thistechnique, an amino acid residue is replaced by Ala, and its effect onthe peptide's activity is determined. Each of the amino acid residues ofthe peptide is analyzed in this manner to determine the importantregions of the peptide.

It is also possible to isolate a target-specific antibody, selected by afunctional assay, and then to solve its crystal structure. In principle,this approach yields a pharmacophore upon which subsequent drug designcan be based.

One can bypass protein crystallography altogether by generatinganti-idiotypic antibodies (anti-ids) to a functional, pharmacologicallyactive antibody. As a mirror image of a mirror image, the binding siteof the anti-ids would be expected to be an analog of the originalmolecule. The anti-id could then be used to identify and isolatepeptides from banks of chemically or biologically produced banks ofpeptides. Selected peptides would then act as the pharmacophore.

Thus, one may design drugs which have, e.g., improved polypeptideactivity or stability or which act as inhibitors, agonists, antagonists,etc. of polypeptide activity. By virtue of the availability of CNVcontaining nucleic acid sequences described herein, sufficient amountsof the encoded polypeptide may be made available to perform suchanalytical studies as x-ray crystallography. In addition, the knowledgeof the protein sequence provided herein will guide those employingcomputer modeling techniques in place of, or in addition to x-raycrystallography.

In another embodiment, the availability of T1D-associated CNV containingnucleic acids enables the production of strains of laboratory micecarrying the T1D-associated CNVs of the invention. Transgenic miceexpressing the T1D-associated CNV of the invention provide a modelsystem in which to examine the role of the protein encoded by the CNVcontaining nucleic acid in the development and progression towards T1D.Methods of introducing transgenes in laboratory mice are known to thoseof skill in the art. Three common methods include: (1) integration ofretroviral vectors encoding the foreign gene of interest into an earlyembryo; (2) injection of DNA into the pronucleus of a newly fertilizedegg; and (3) the incorporation of genetically manipulated embryonic stemcells into an early embryo. Production of the transgenic mice describedabove will facilitate the molecular elucidation of the role that atarget protein plays in various cellular metabolic processes, including:aberrant lipid deposition, altered cellular metabolism and glucoseregulation. Such mice provide an in vivo screening tool to studyputative therapeutic drugs in a whole animal model and are encompassedby the present invention.

The term “animal” is used herein to include all vertebrate animals,except humans. It also includes an individual animal in all stages ofdevelopment, including embryonic and fetal stages. A “transgenic animal”is any animal containing one or more cells bearing genetic informationaltered or received, directly or indirectly, by deliberate geneticmanipulation at the subcellular level, such as by targeted recombinationor microinjection or infection with recombinant virus. The term“transgenic animal” is not meant to encompass classical cross-breedingor in vitro fertilization, but rather is meant to encompass animals inwhich one or more cells are altered by or receive a recombinant DNAmolecule. This molecule may be specifically targeted to a definedgenetic locus, be randomly integrated within a chromosome, or it may beextra-chromosomally replicating DNA. The term “germ cell line transgenicanimal” refers to a transgenic animal in which the genetic alteration orgenetic information was introduced into a germ line cell, therebyconferring the ability to transfer the genetic information to offspring.If such offspring, in fact, possess some or all of that alteration orgenetic information, then they, too, are transgenic animals.

The alteration of genetic information may be foreign to the species ofanimal to which the recipient belongs, or foreign only to the particularindividual recipient, or may be genetic information already possessed bythe recipient. In the last case, the altered or introduced gene may beexpressed differently than the native gene. Such altered or foreigngenetic information would encompass the introduction of T1D-associatedCNV containing nucleotide sequences.

The DNA used for altering a target gene may be obtained by a widevariety of techniques that include, but are not limited to, isolationfrom genomic sources, preparation of cDNAs from isolated mRNA templates,direct synthesis, or a combination thereof.

A preferred type of target cell for transgene introduction is theembryonal stem cell (ES). ES cells may be obtained from pre-implantationembryos cultured in vitro (Evans et al., (1981) Nature 292:154-156;Bradley et al., (1984) Nature 309:255-258; Gossler et al., (1986) Proc.Natl. Acad. Sci. 83:9065-9069). Transgenes can be efficiently introducedinto the ES cells by standard techniques such as DNA transfection or byretrovirus-mediated transduction. The resultant transformed ES cells canthereafter be combined with blastocysts from a non-human animal. Theintroduced ES cells thereafter colonize the embryo and contribute to thegerm line of the resulting chimeric animal.

One approach to the problem of determining the contributions ofindividual genes and their expression products is to use isolatedT1D-associated CNV genes as insertional cassettes to selectivelyinactivate a wild-type gene in totipotent ES cells (such as thosedescribed above) and then generate transgenic mice. The use ofgene-targeted ES cells in the generation of gene-targeted transgenicmice was described, and is reviewed elsewhere (Frohman et al., (1989)Cell 56:145-147; Bradley et al., (1992) Bio/Technology 10:534-539).

Techniques are available to inactivate or alter any genetic region to amutation desired by using targeted homologous recombination to insertspecific changes into chromosomal alleles. However, in comparison withhomologous extra-chromosomal recombination, which occurs at a frequencyapproaching 100%, homologous plasmid-chromosome recombination wasoriginally reported to only be detected at frequencies between 10⁻⁶ and10⁻³. Non-homologous plasmid-chromosome interactions are more frequentoccurring at levels 10⁵-fold to 10² fold greater than comparablehomologous insertion.

To overcome this low proportion of targeted recombination in murine EScells, various strategies have been developed to detect or select rarehomologous recombinants. One approach for detecting homologousalteration events uses the polymerase chain reaction (PCR) to screenpools of transformant cells for homologous insertion, followed byscreening of individual clones. Alternatively, a positive geneticselection approach has been developed in which a marker gene isconstructed which will only be active if homologous insertion occurs,allowing these recombinants to be selected directly. One of the mostpowerful approaches developed for selecting homologous recombinants isthe positive-negative selection (PNS) method developed for genes forwhich no direct selection of the alteration exists. The PNS method ismore efficient for targeting genes which are not expressed at highlevels because the marker gene has its own promoter. Non-homologousrecombinants are selected against by using the Herpes Simplex virusthymidine kinase (HSV-TK) gene and selecting against its nonhomologousinsertion with effective herpes drugs such as gancyclovir (GANC) or(1-(2-deoxy-2-fluoro-B-D arabinofluranosyl)-5-iodou-racil, (FIAU). Bythis counter selection, the number of homologous recombinants in thesurviving transformants can be increased. Utilizing T1D-associated CNVcontaining nucleic acid as a targeted insertional cassette providesmeans to detect a successful insertion as visualized, for example, byacquisition of immunoreactivity to an antibody immunologically specificfor the polypeptide encoded by T1D-associated CNV nucleic acid and,therefore, facilitates screening/selection of ES cells with the desiredgenotype.

As used herein, a knock-in animal is one in which the endogenous murinegene, for example, has been replaced with human T1D-associated CNVcontaining gene of the invention. Such knock-in animals provide an idealmodel system for studying the development of T1D.

As used herein, the expression of a T1D-associated CNV containingnucleic acid, fragment thereof, or a T1D-associated CNV fusion proteincan be targeted in a “tissue specific manner” or “cell type specificmanner” using a vector in which nucleic acid sequences encoding all or aportion of T1D-associated CNV are operably linked to regulatorysequences (e.g., promoters and/or enhancers) that direct expression ofthe encoded protein in a particular tissue or cell type. Such regulatoryelements may be used to advantage for both in vitro and in vivoapplications. Promoters for directing tissue specific expression ofproteins are well known in the art and described herein.

The nucleic acid sequence encoding the T1D-associated CNV of theinvention may be operably linked to a variety of different promotersequences for expression in transgenic animals. Such promoters include,but are not limited to a platelet-derived growth factor B gene promoter,described in U.S. Pat. No. 5,811,633; a brain specific dystrophinpromoter, described in U.S. Pat. No. 5,849,999; a Thy-1 promoter; a PGKpromoter; a CMV promoter; a neuronal-specific platelet-derived growthfactor B gene promoter; and Glial fibrillar acidic protein (GFAP)promoter for the expression of transgenes in glial cells.

Methods of use for the transgenic mice of the invention are alsoprovided herein. Transgenic mice into which a nucleic acid containingthe T1D-associated CNV or its encoded protein have been introduced areuseful, for example, to develop screening methods to screen therapeuticagents to identify those capable of modulating the development of T1D.

Pharmaceuticals and Peptide Therapies

The elucidation of the role played by the T1D associated CNVs describedherein in cellular and glucose metabolism facilitates the development ofpharmaceutical compositions useful for treatment and diagnosis of T1D.These compositions may comprise, in addition to one of the abovesubstances, a pharmaceutically acceptable excipient, carrier, buffer,stabilizer or other materials well known to those skilled in the art.Such materials should be non-toxic and should not interfere with theefficacy of the active ingredient.

Whether it is a polypeptide, antibody, peptide, nucleic acid molecule,small molecule or other pharmaceutically useful compound according tothe present invention that is to be given to an individual,administration is preferably in a “prophylactically effective amount” ora “therapeutically effective amount” (as the case may be, althoughprophylaxis may be considered therapy), this being sufficient to showbenefit to the individual.

As it is presently understood, RNA interference involves a multi-stepprocess. Double stranded RNAs are cleaved by the endonuclease Dicer togenerate nucleotide fragments (siRNA). The siRNA duplex is resolved into2 single stranded RNAs, one strand being incorporated into aprotein-containing complex where it functions as guide RNA to directcleavage of the target RNA (Schwarz et al, Mol. Cell. 10:537 548 (2002),Zamore et al, Cell 101:25 33 (2000)), thus silencing a specific geneticmessage (see also Zeng et al, Proc. Natl. Acad. Sci. 100:9779 (2003)).

The invention includes a method of treating T1D in a mammal. Anexemplary method entails administering to the mammal a pharmaceuticallyeffective amount of a siRNA specific for a gene target listed inTable 1. The siRNA inhibits the expression of target gene of interest.Preferably, the mammal is a human. The term “patient” as used hereinrefers to a human.

Specific siRNA preparations directed at inhibiting the expression of atarget gene listed in Table 1, as well as delivery methods are providedas a novel therapy to treat T1D. SiRNA oligonucleotides directed to thetarget gene of interest specifically hybridize with nucleic acidsencoding the target gene product and interfere with target geneexpression. The siRNA can be delivered to a patient in vivo eithersystemically or locally with carriers, as discussed below. Thecompositions of the invention may be used alone or in combination withother agents or genes encoding proteins to augment the efficacy of thecompositions.

A “membrane permeant peptide sequence” refers to a peptide sequencewhich is able to facilitate penetration and entry of the target genespecific inhibitor across the cell membrane. Exemplary peptides includewith out limitation, the signal sequence from Karposi fibroblast growthfactor exemplified herein, the HIV tat peptide (Vives et al., J Biol.Chem., 272:16010-16017, 1997), Nontoxic membrane translocation peptidefrom protamine (Park et al., FASEB J. 19(11):1555-7, 2005), CHARIOT®delivery reagent (Active Motif; U.S. Pat. No. 6,841,535) and theantimicrobial peptide Buforin 2.

In one embodiment of the invention siRNAs are delivered for therapeuticbenefit. There are several ways to administer the siRNA of the inventionto in vivo to treat T1D including, but not limited to, naked siRNAdelivery, siRNA conjugation and delivery, liposome carrier-mediateddelivery, polymer carrier delivery, nanoparticle compositions,plasmid-based methods, and the use of viruses.

siRNA composition of the invention can comprise a delivery vehicle,including liposomes, for administration to a subject, carriers anddiluents and their salts, and/or can be present in pharmaceuticallyacceptable formulations. This can be necessary to allow the siRNA tocross the cell membrane and escape degradation. Methods for the deliveryof nucleic acid molecules are described in Akhtar et al., 1992, TrendsCell Bio., 2, 139; Delivery Strategies for Antisense OligonucleotideTherapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol.,16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137,165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192; Beigelmanet al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595further describe the general methods for delivery of nucleic acidmolecules. These protocols can be utilized for the delivery of virtuallyany nucleic acid molecule.

The frequency of administration of the siRNA to a patient will also varydepending on several factors including, but not limited to, the type andseverity of the T1D to be treated, the route of administration, the ageand overall health of the individual, the nature of the siRNA, and thelike. It is contemplated that the frequency of administration of thesiRNA to the patient may vary from about once every few months to aboutonce a month, to about once a week, to about once per day, to aboutseveral times daily.

Pharmaceutical compositions that are useful in the methods of theinvention may be administered systemically in parenteral, oral solid andliquid formulations, ophthalmic, suppository, aerosol, topical or othersimilar formulations. In addition to the appropriate siRNA, thesepharmaceutical compositions may contain pharmaceutically-acceptablecarriers and other ingredients known to enhance and facilitate drugadministration. Thus such compositions may optionally contain othercomponents, such as adjuvants, e.g., aqueous suspensions of aluminum andmagnesium hydroxides, and/or other pharmaceutically acceptable carriers,such as saline. Other possible formulations, such as nanoparticles,liposomes, resealed erythrocytes, and immunologically based systems mayalso be used to administer the appropriate siRNA to a patient accordingto the methods of the invention. The use of nanoparticles to deliversiRNAs, as well as cell membrane permeable peptide carriers that can beused are described in Crombez et al., Biochemical Society Transactionsv35:p44 (2007).

Methods of the invention directed to treating T1D involve theadministration of a target gene specific siRNA in a pharmaceuticalcomposition. Such siRNA is administered to an individual as apharmaceutical composition comprising the siRNA and a pharmaceuticallyacceptable carrier. Pharmaceutically acceptable carriers are well knownin the art and include aqueous solutions such as physiologicallybuffered saline, other solvents or vehicles such as glycols, glycerol,oils such as olive oil or injectable organic esters.

A pharmaceutically acceptable carrier can contain physiologicallyacceptable compounds that act, for example, to stabilize the siRNA orincrease the absorption of the agent. Such physiologically acceptablecompounds include, for example, carbohydrates, such as glucose, sucroseor dextrans, antioxidants, such as ascorbic acid or glutathione,chelating agents, low molecular weight proteins or other stabilizers orexcipients. One skilled in the art would know that the choice of apharmaceutically acceptable carrier, including a physiologicallyacceptable compound, depends, for example, on the route ofadministration of the siRNA.

One skilled in the art appreciates that a pharmaceutical compositioncomprising siRNA can be administered to a subject by various routesincluding, for example, orally or parenterally, such as intravenously(i.v.), intramuscularly, subcutaneously, intraorbitally, intranasally,intracapsularly, intraperitoneally (i.p.), intracistemally,intra-tracheally (i.t.), or intra-articularly or by passive orfacilitated absorption. The same routes of administration can be usedother pharmaceutically useful compounds, for example, small molecules,nucleic acid molecules, peptides, antibodies and polypeptides asdiscussed hereinabove.

A pharmaceutical composition comprising siRNA inhibitor also can beincorporated, if desired, into liposomes, microspheres, microbubbles, orother polymer matrices (Gregoriadis, Liposome Technology, Vols. I toIII, 2nd ed., CRC Press, Boca Raton Fla. (1993)). Liposomes, forexample, which consist of phospholipids or other lipids, are nontoxic,physiologically acceptable and metabolizable carriers that arerelatively simple to make and administer.

The pharmaceutical preparation comprises a siRNA targeting a gene listedin Table 1 or an expression vector encoding for said siRNA. Suchpharmaceutical preparations can be administered to a patient fortreating T1D.

Expression vectors for the expression of siRNA molecules preferablyemploy a strong promoter which may be constitutive or regulated. Suchpromoters are well known in the art and include, but are not limited to,RNA polymerase II promoters, the T7 RNA polymerase promoter, and the RNApolymerase III promoters U6 and H1 (see, e.g., Myslinski et al. (2001)Nucl. Acids Res., 29:2502 09).

A formulated siRNA composition can be a composition comprising one ormore siRNA molecules or a vector encoding one or more siRNA moleculesindependently or in combination with a cationic lipid, a neutral lipid,and/or a polyethyleneglycol-diacylglycerol (PEG-DAG) or PEG-cholesterol(PEG-Chol) conjugate. Non-limiting examples of expression vectors aredescribed in Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishiand Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, NatureBiotechnology, 19, 500-505.

A lipid nanoparticle composition is a composition comprising one or morebiologically active molecules independently or in combination with acationic lipid, a neutral lipid, and/or apolyethyleneglycol-diacylglycerol (i.e., polyethyleneglycoldiacylglycerol (PEG-DAG), PEG-cholesterol, or PEG-DMB) conjugate. In oneembodiment, the biologically active molecule is encapsulated in thelipid nanoparticle as a result of the process of providing and aqueoussolution comprising a biologically active molecule of the invention(i.e., siRNA), providing an organic solution comprising lipidnanoparticle, mixing the two solutions, incubating the solutions,dilution, ultrafiltration, resulting in concentrations suitable toproduce nanoparticle compositions.

Nucleic acid molecules can be administered to cells by incorporationinto other vehicles, such as biodegradable polymers, hydrogels,cyclodextrins. (see for example Gonzalez et al., 1999, BioconjugateChem., 10, 1068-1074; Wang et al., International PCT publication Nos. WO03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCAmicrospheres (see for example U.S. Pat. No. 6,447,796 and US PatentApplication Publication No. US 2002130430), biodegradable nanocapsules,and bioadhesive microspheres, or by proteinaceous vectors (O'Hare andNormand, International PCT Publication No. WO 00/53722)

Cationic lipids and polymers are two classes of non-viral siRNA deliverywhich can form complexes with negatively charged siRNA. Theself-assembly PEG-ylated polycation polyethylenimine (PEI) has also beenused to condense and protect siRNAs (Schiffelers et al., 2004, Nuc.Acids Res. 32: 141-110). The siRNA complex can be condensed into ananoparticle to allow efficient uptake of the siRNA through endocytosis.Also, the nucleic acid-condensing property of protamine has beencombined with specific antibodies to deliver siRNAs and can be used inthe invention (Song et al., 2005, Nat Biotech. 23:709-717).

In order to treat an individual having T1D, to alleviate a sign orsymptom of the disease, the siRNA should be administered in an effectivedose. The total treatment dose can be administered to a subject as asingle dose or can be administered using a fractionated treatmentprotocol, in which multiple doses are administered over a more prolongedperiod of time, for example, over the period of a day to allowadministration of a daily dosage or over a longer period of time toadminister a dose over a desired period of time. One skilled in the artwould know that the amount of siRNA required to obtain an effective dosein a subject depends on many factors, including the age, weight andgeneral health of the subject, as well as the route of administrationand the number of treatments to be administered. In view of thesefactors, the skilled artisan would adjust the particular dose so as toobtain an effective dose for treating an individual having T1D.

The effective dose of siRNA will depend on the mode of administration,and the weight of the individual being treated. The dosages describedherein are generally those for an average adult but can be adjusted forthe treatment of children. The dose will generally range from about0.001 mg to about 1000 mg.

The concentration of siRNA in a particular formulation will depend onthe mode and frequency of administration. A given daily dosage can beadministered in a single dose or in multiple doses so long as the siRNAconcentration in the formulation results in the desired daily dosage.One skilled in the art can adjust the amount of siRNA in the formulationto allow administration of a single dose or in multiple doses thatprovide the desired concentration of siRNA over a given period of time.

In an individual suffering from T1D, in particular a more severe form ofthe disease, administration of siRNA can be particularly useful whenadministered in combination, for example, with a conventional agent fortreating such a disease. The skilled artisan would administer siRNA,alone or in combination and would monitor the effectiveness of suchtreatment using routine methods such as pulmonary functiondetermination, radiologic, immunologic or, where indicated,histopathologic methods. Other conventional agents for the treatment ofdiabetes include insulin administration, glucagon administration oragents that alter levels of either of these two molecules. Glucophage®,Avandia®, Actos®, Januvia® and Glucovance® are examples of such agents.

Administration of the pharmaceutical preparation is preferably in an“effective amount” this being sufficient to show benefit to theindividual. This amount prevents, alleviates, abates, or otherwisereduces the severity of T1D symptoms in a patient.

The pharmaceutical preparation is formulated in dosage unit form forease of administration and uniformity of dosage. Dosage unit form, asused herein, refers to a physically discrete unit of the pharmaceuticalpreparation appropriate for the patient undergoing treatment. Eachdosage should contain a quantity of active ingredient calculated toproduce the desired effect in association with the selectedpharmaceutical carrier. Procedures for determining the appropriatedosage unit are well known to those skilled in the art.

Dosage units may be proportionately increased or decreased based on theweight of the patient. Appropriate concentrations for alleviation of aparticular pathological condition may be determined by dosageconcentration curve calculations, as known in the art.

The following examples are provided to illustrate certain embodiments ofthe invention. They are not intended to limit the invention in any way.

Example I Identification of CNVs Associated with TId in a PediatricGenome Wide Association Study

We recently completed a genome-wide search for copy number variation(CNV) association with the Type 1 Diabetes (T1D) phenotype. The dataquality was strictly filtered based on a call rate above 98%,populations of cases and controls which closely stratified based onAncestry Informative Markers (AIMs) clustering, a standard deviation ofnormalized intensity below 0.35, low waviness of intensity correspondingwith GC content, and a maximum count of 40 CNVs per individual. Thisresulted in 504 T1D cases, 292 with complete trios and 3979 disease-freecontrols. Utilizing a Hidden Markov Model (HMM) approach implemented byPennCNV (Wang et al, 2007), the most probable CNV state is reported fora contiguous sequence of SNPs for each individual sample. We firstsearched for evidence for association of CNVs to any of the previouslyreported genes that associate with T1D, including but not limited toHLA, INS, PTPN22, CTLA4, KIAA0350 (CLEC16A) PARP1, AGER, and C4A. Therewas no evidence for CNV association to these specific genes. SNP basedwhole genome CNV association was subsequently preformed to capture themost significant points in complex CNV overlap between case and controlpopulations. A chi square statistic is applied to the CNV observance ofdeletion and duplication for each SNP. To present results in anon-redundant manner, statistical local minimums are reported inreference to a region of nominal significance including SNPs residingwithin 1 MB. We identified regions of deletion and duplication (Table 1)CNVs in T1D using this approach. The most biologically relevant topreviously associated T1D pathways are: MAML2, BAK1, CCND1, RERGL,RNASE4, TRPM1, ANBPT1, ETS2, RAB27A, PYGO1, TBC1, DDEF1, SBF2, PTPRT,COL1A1, NGFR, ALPP, KCNS3, KCNK2, TMTC1, MCTP2, PRSS3, SCG, ONECUT1,AK055863, ETV3, EPX, CRLF3, IGFBP4, SORBS1, and BCMO1.

After review, 47 CNV regions that included at least 2 CNV observancesvalidated, of whom 29 resided on genes. To address the potentialbiological role of these results, functional clustering of independentlyassociated and validated results provided: Immune system (3 loci, 7 CNVsp=1.9×10⁻⁴), Insulin (2 loci, 4 CNVs p=1.6×10⁻³), Pancreas or liverexpression (4 loci, 8 CNVs p=2.3×10⁻³), CNS development (5 loci, 16CNVs, p=1.0×10⁻⁶), Vitamin A (1 loci, 3 CNVs 5.2×10⁻³), Cell cyclesignaling (10 loci, 29 CNVs p=8.0×10⁻⁷), and Membrane channels (4 loci,13 CNVs p=1.6×10⁻⁵).

Taken together, we have identified 29 genes harboring 80 CNVs inpreviously associated T1D pathways that involve 70 cases and thus couldaccount for up to 14% of T1D cases. These results suggest that thegenetic landscape in the pathogenesis of T1D involves both common andrare CNVs that associate with the T1D phenotypes, where the rare CNVsare highly heterogeneous and unique to the individual families andcluster on genes that are involved with endocrine signaling anddevelopment.

TABLE 1 High Confidence associations of loci to 2 or more T1D cases GeneCs- Co- Family CNVR B36 Gene B36 Dist Pvalue CN Cs Di Co Di Cellchr11:95619379-95620715 MAML2 0 0.0026 Del 9 495 19  3961 Cycle geneCell chr6:33604692-33633658 BAK 14643 0.0052 Del 3 501 1 3978 Cycle geneCell chr11:69172091-69178211 CCND1 0 0.035 Del 2 502 1 3977 Cycle geneCell chr12:18117011-18207216 RERGL 0 0.0126 Del 2 502 0 3978 Cycle geneCell chr14:20179566-20252640 ANG 0 0.3125 Del 2 502 8 3970 Cycle geneCell chr15:29143717-29172089 TRPM1 0 0.0126 Del 2 502 0 3978 Cycle geneCell chr8:107736969-108423211 ANGPT1 0 0.3125 Del 2 502 8 3968 Cyclegene Cell chr21:39037914-39074242 ETS2 25477 0.0126 Dup 2 502 0 3978Cycle gene Cell chr15:53348055-53717834 RAB27A 0 0.0119 Dup 3 501 2 3977Cycle gene Cell chr22:45875872-45882946 TBC1D22A 0 0.0649 Dup 2 502 23977 Cycle gene CNS chr8:131388051-131428826 DDEF1 0 0.0052 Del 3 501 13978 Develop- ment CNS chr11:9907833-9929638 SBF2 0 0.0052 Del 3 501 13978 Develop- ment CNS chr20:40615725-40718196 PTPRT 0 0.3122 Del 2 5028 3971 Develop- ment CNS chr17:44875052-45629290 COL1A1 0 0.0126 Del 2502 0 3974 Develop- ment CNS chr2:232936077-233023552 ALPP 0 0.0006 Dup6 498 5 3967 Develop- ment Mem- chr2:18048653-18056323 KCNS3 709470.0001 Del 6 498 3 3972 brane channel Mem- chr1:213463166-213468645KCNK2 0 0.0119 Del 3 501 2 3975 brane channel Mem-chr12:29906457-29906761 TMTC1 77498 0.2687 Del 2 502 7 3968 branechannel Mem- chr15:91967763-92629470 MCTP2 0 0.0351 Del 2 502 1 3976brane channel Pancreas/ chr9:33774908-33835079 PRSS3 0 0.035 Dup 2 502 13978 Liver Pancreas/ chr11:61744703-61760148 SCGB1D2 6152 0.0126 Dup 2502 0 3978 Liver Pancreas/ chr15:50785554-50804739 ONECUT1 23661 0.1003Dup 2 502 3 3973 Liver Pancreas/ chr8:9217544-9304527 AK055863 0 0.1397Dup 2 502 4 3969 Liver Immune chr1:155423036-155427970 ETV3 48235 0.0126Del 2 502 0 3978 System Immune chr17:53625120-53626496 EPX 0 0.0126 Del2 502 0 3974 System Immune chr17:26040486-26188149 CRLF3 0 0.0119 Dup 3501 2 3977 System Insulin chr17:35862733-35871630 IGFBP4 0 0.0126 Del 2502 0 3975 Insulin chr10:97127095-97391986 SORBS1 0 0.0126 Dup 2 502 03977 Vitamin chr16:79822098-79838201 BCDO 0 0.0052 Del 3 500 1 3976 ADist: Distance B-36; Cs: Cases; Cs-Di: Cases Diploid; Co: Control;Co-Di: Control Diploid

Example II

The information herein above can be applied clinically to patients fordiagnosing an increased susceptibility for developing T1D, andtherapeutic intervention. A preferred embodiment of the inventioncomprises clinical application of the information described herein to apatient. Diagnostic compositions, including microarrays, and methods canbe designed to identify the genetic alterations described herein innucleic acids from a patient to assess susceptibility for developingT1D. This can occur after a patient arrives in the clinic; the patienthas blood drawn, and using the diagnostic methods described herein, aclinician can detect a CNV in at least one of the gene products listedin Table 1 above. The typical age range for a patient to be screened isbetween 9 and 12 years of age. The information obtained from the patientsample, which can optionally be amplified prior to assessment, will beused to diagnose a patient with an increased susceptibility fordeveloping T1D. Kits for performing the diagnostic method of theinvention are also provided herein. Such kits comprise a microarraycomprising at least one of the CNVs provided herein in and the necessaryreagents for assessing the patient samples as described above.

The identity of T1D-involved genes and the patient results will indicatewhich variants are present, and will identify those that possess analtered risk for developing T1D. The information provided herein allowsfor therapeutic intervention at earlier times in disease progressionthat previously possible. Also as described herein above, the geneslisted in Table 1 provide novel targets for the development of newtherapeutic agents efficacious for the treatment of T1D. For example,the therapeutic siRNAs described herein can be used to block expressionof the gene product based on the patient signal, thereby inhibiting thepancreatic β-cell destruction that occurs in T1D.

REFERENCES

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While certain of the preferred embodiments of the present invention havebeen described and specifically exemplified above, it is not intendedthat the invention be limited to such embodiments. It will be apparentto one skilled in the art that various changes and modifications can bemade therein without departing from the scope of the present invention,as set forth in the following claims.

1. A method for detecting the presence or absence of at least onegenetic alteration in a target nucleic acid isolated from a patient forassessing susceptibility for developing type 1 diabetes (T1D), saidmethod comprising: a) providing a target nucleic acid from a patientsample, said target nucleic acid having a predetermined sequence in thenormal population; b) assessing said target nucleic acid for thepresence of a copy number variation which is indicative of an increasedsusceptibility of developing T1D.
 2. The method as claimed in claim 1,wherein said genetic alteration is selected from the group consisting ofa deletion, or a duplication of at least one nucleotide in saidsequence.
 3. The method of claim 1, wherein said target nucleic acid isassessed for genetic alterations via a method selected from the groupconsisting of size analysis, hybridization of allele specific probes,allele-specific primer extension, oligomer ligation, DNA sequencing,single-stranded conformation polymorphism, and quantitative PCR.
 4. Themethod as claimed in claim 1, wherein said genetic alteration is atleast one copy number variation (CNV) present in a gene listed inTable
 1. 5. A kit for practicing the method of claim
 1. 6. A nucleicacid comprising at least one CNV identified in Table
 1. 7. A microarraycomprising the at least one nucleic acid of claim 6, said nucleic acidoptionally being between 10 and 50 nucleotides in length.
 8. A method ofmanagement for T1D comprising: a) identifying a patient who is at anincreased risk of developing T1D by detecting at least one of the CNVsin Table 1; b) administering to said patient a therapeutic agent in atherapeutically effective amount to manage T1D.
 9. The method accordingto claim 8, wherein said therapeutic agent is selected from the groupconsisting of a small molecule, an antibody, a protein, anoligonucleotide, or an siRNA molecule.
 10. The method of claim 9,wherein said therapeutic agent is delivered to an inflammatory cell. 11.The method of claim 9, wherein said therapeutic agent modulates naturalkiller cell activity.
 12. The method of claim 9, wherein saidtherapeutic agent modulates signaling in an insulin-producing beta cell.13. The method of claim 12, wherein modulatory effects of said agent areassessed on a parameter selected from the group consisting of insulinsecretion, glucagon secretion and glucosamine induced beta cellapoptosis is determined.
 14. The method as claimed in claim 4 whereinsaid gene is selected from the group consisting of CCND1, REGL, TRPM1and KCNS3.
 15. The method as claimed in claim 8 wherein said gene isselected from the group consisting of CCND1, REGL, TRPM1 and KCNS3. 16.The method as claimed in claim 4 wherein said gene is IGFBP4.
 17. Themethod as claimed in claim 8 wherein said gene is selected from thegroup consisting of IGFBP4.